Public Member Functions
def	__init__ (self, ent, dist_thresh=15.0, dist_diff_thresholds=[0.5, 1.0, 2.0, 4.0])

def	view (self)

def	dist_thresh (self)

def	dist_diff_thresholds (self)

def	chain_names (self)

def	interacting_chains (self)

def	potentially_contributing_chains (self)

def	n_pair_contacts (self)

def	n_sc_contacts (self)

def	n_contacts (self)

def	GetChain (self, chain_name)

def	GetSequence (self, chain_name)

def	GetPos (self, chain_name)

def	Dist (self, chain_name)

def	PairDist (self, chain_name_one, chain_name_two)

def	GetMinPos (self, chain_name)

def	GetMaxPos (self, chain_name)

def	PotentialInteraction (self, chain_name_one, chain_name_two, slack=0.0)

Detailed Description

 Helper object for BBlDDT computation

Holds structural information and getters for interacting chains, i.e.
interfaces. Peptide residues are represented by their CA position
and nucleotides by C3'.

:param ent: Structure for BBlDDT score computation
:type ent: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param contact_d: Pairwise distance of residues to be considered as contacts
:type contact_d: :class:`float`

Definition at line 8 of file bb_lddt.py.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		ent,
		dist_thresh = `15.0`,
		dist_diff_thresholds = `[0.5, 1.0, 2.0, 4.0]`
	)

Definition at line 20 of file bb_lddt.py.

Member Function Documentation

◆ chain_names()

def chain_names ( self )

 Chain names in :attr:`~view`

Names are sorted

:type: :class:`list` of :class:`str`

Definition at line 76 of file bb_lddt.py.

◆ Dist()

def Dist	(	self,
		chain_name
	)

 Get pairwise distance of residues within same chain

Returns distances as square numpy array of shape (a,a)
where a is the number of residues in specified chain.

Definition at line 212 of file bb_lddt.py.

◆ dist_diff_thresholds()

def dist_diff_thresholds ( self )

 Distance difference thresholds for lDDT computation

Given at :class:`BBlDDTEntity` construction

:type: :class:`list` of :class:`float`

Definition at line 66 of file bb_lddt.py.

◆ dist_thresh()

def dist_thresh ( self )

 Pairwise distance of residues to be considered as contacts

Given at :class:`BBlDDTEntity` construction

:type: :class:`float`

Definition at line 56 of file bb_lddt.py.

◆ GetChain()

def GetChain	(	self,
		chain_name
	)

 Get chain by name

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 169 of file bb_lddt.py.

◆ GetMaxPos()

def GetMaxPos	(	self,
		chain_name
	)

 Get max x,y,z cooridnates for given chain

Based on positions that are extracted with GetPos

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 251 of file bb_lddt.py.

◆ GetMinPos()

def GetMinPos	(	self,
		chain_name
	)

 Get min x,y,z cooridnates for given chain

Based on positions that are extracted with GetPos

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 239 of file bb_lddt.py.

◆ GetPos()

def GetPos	(	self,
		chain_name
	)

 Get representative positions of chain

That's CA positions for peptide residues and C3' for
nucleotides. Returns positions as a numpy array of shape
(n_residues, 3).

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 194 of file bb_lddt.py.

◆ GetSequence()

def GetSequence	(	self,
		chain_name
	)

 Get sequence of chain

Returns sequence of specified chain as raw :class:`str`

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 180 of file bb_lddt.py.

◆ interacting_chains()

def interacting_chains ( self )

 Pairs of chains in :attr:`~view` with at least one contact

:type: :class:`list` of :class:`tuples`

Definition at line 88 of file bb_lddt.py.

◆ n_contacts()

def n_contacts ( self )

 Total number of contacts

That's the sum of all :attr:`~n_pair_contacts` and
:attr:`~n_sc_contacts`.

:type: :class:`int`

Definition at line 157 of file bb_lddt.py.

◆ n_pair_contacts()

def n_pair_contacts ( self )

 Number of contacts in :attr:`~interacting_chains`

:type: :class:`list` of :class:`int`

Definition at line 128 of file bb_lddt.py.

◆ n_sc_contacts()

def n_sc_contacts ( self )

 Number of contacts for single chains in :attr:`~chain_names`

:type: :class:`list` of :class:`int`

Definition at line 140 of file bb_lddt.py.

◆ PairDist()

def PairDist	(	self,
		chain_name_one,
		chain_name_two
	)

 Get pairwise distances between two chains

Returns distances as numpy array of shape (a, b).
Where a is the number of residues of the chain that comes BEFORE the
other in :attr:`~chain_names`

Definition at line 224 of file bb_lddt.py.

◆ PotentialInteraction()

def PotentialInteraction	(	self,
		chain_name_one,
		chain_name_two,
		slack = `0.0`
	)

 Returns True if chains potentially interact

Based on crude collision detection. There is no guarantee
that they actually interact if True is returned. However,
if False is returned, they don't interact for sure.

:param chain_name_one: Chain in :attr:`~view`
:type chain_name_one: class:`str`
:param chain_name_two: Chain in :attr:`~view`
:type chain_name_two: class:`str`
:param slack: Add slack to interaction distance threshold
:type slack: :class:`float`

Definition at line 263 of file bb_lddt.py.

◆ potentially_contributing_chains()

def potentially_contributing_chains ( self )

 Pairs of chains in :attr:`view` with potential contribution to lDDT

That are pairs of chains that have at least one interaction within
:attr:`~dist_thresh` + max(:attr:`~dist_diff_thresholds`)

Definition at line 108 of file bb_lddt.py.

◆ view()

def view ( self )

 Processed structure

View that only contains representative atoms. That's CA for peptide
residues and C3' for nucleotides.

:type: :class:`ost.mol.EntityView`

Definition at line 45 of file bb_lddt.py.

The documentation for this class was generated from the following file:

build-dev-doc/stage/lib64/python3.9/site-packages/ost/mol/alg/bb_lddt.py

Public Member Functions